Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add tondevrel/scientific-agent-skills --skill openbabelgit clone --depth 1 https://github.com/tondevrel/scientific-agent-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/tondevrel/scientific-agent-skills/openbabel)<a href="https://agentmods.dev/skills/tondevrel/scientific-agent-skills/openbabel"><img src="https://agentmods.dev/badge/skills/tondevrel/scientific-agent-skills/openbabel/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/tondevrel/scientific-agent-skills/openbabel"><img src="https://agentmods.dev/badge/skills/tondevrel/scientific-agent-skills/openbabel.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00116 | $0.02709 |
| Opus 5 | $0.00058 | $0.01354 |
| Sonnet 5 | $0.00023 | $0.00542 |
| Haiku 4.5 | $0.00012 | $0.00271 |
Grade A, and why
openbabel scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 308 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Open Babel - The Universal Chemical Translator
Open Babel (and its Python wrapper pybel) is the essential tool for chemical data interoperability. It allows researchers to seamlessly move data between formats like SMILES, PDB, SDF, CIF, and Gaussian input/output.
When to Use
- Converting chemical files between different formats (e.g., SDF to PDB).
- Generating 3D coordinates from 2D structures or SMILES.
- Searching for substructures using SMARTS patterns.
- Performing fast molecular docking preparation (e.g., adding hydrogens, calculating charges).
- Running basic force field minimizations (UFF, GAFF, MMFF94).
- Calculating molecular fingerprints and Tanimoto coefficients.
- Batch processing large chemical databases (millions of molecules).
Reference Documentation
Official docs: https://openbabel.org/docs/dev/
Python API (Pybel): https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html
Search patterns: openbabel.OBMol, pybel.readfile, pybel.readstring, mol.make3D
Core Principles
OB vs. Pybel
- OpenBabel (SWIG): Низкоуровневый интерфейс, прямой доступ к C++ классам (OBMol, OBAtom). Сложный, но максимально мощный.
- Pybel: Высокоуровневая «обертка», более Pythonic-стиль. Рекомендуется для 90% задач.
The Conversion Engine
Open Babel работает как конвейер: Input Format -> Internal OBMol -> Output Format. Вы можете добавлять фильтры и трансформации (удаление солей, добавление водородов) прямо в процессе конвертации.
Quick Reference
Installation
# Recommended via conda/mamba
conda install -c conda-forge openbabel
Standard Imports
from openbabel import openbabel as ob
from openbabel import pybel
Basic Pattern - Format Conversion
from openbabel import pybel
# 1. Read molecule (from string or file)
mol = pybel.readstring("smi", "CC(=O)Oc1ccccc1C(=O)O") # Aspirin
# 2. Add metadata
mol.title = "Aspirin_001"
# 3. Write to a different format
output_pdb = mol.write("pdb")
# Or write to file
# mol.write("sdf", "aspirin.sdf", overwrite=True)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 10d ago First seen · 308 lines · 116 tokens per session scan A 2a0e40c27613
openbabel is a skill published in the GitHub repository tondevrel/scientific-agent-skills (21 stars, last pushed 7mo ago), licensed MIT. It adds 116 tokens to every session and 2,709 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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